tbuckley/cabot-search huggingface dataset:
Abstract 5834: Examining the potential oncogenic function of septins and their interaction with Chmp1A tumor suppressor in pancreatic cancer
Authors: Mei Cai, Joseph Amor, Maiyon Park
Journal: Cancer Research (2022)

Abstract Introduction: Chmp1A functions as a tumor suppressor by the activation of ATM and p53 in pancreatic cancer. The nuclear localization signal (NLS) of Chmp1A is required for cell growth inhibition and activation of ATM and p53. Proteomic analysis has identified Septins (a group of GTP-binding proteins) to be associated with the NLS-deleted Chmp1A. Since NLS-deleted Chmp1A promotes cancer cell growth, we hypothesized that Septins may function as oncogenes and that Chmp1A functions as a tumor suppressor partly by inhibiting the oncogenic action of Septin proteins. Objective: To examine whether Septin proteins exhibit oncogenic activity and to investigate whether Chmp1A inhibits the oncogenic function of Septins. Methodology: Using normal pancreatic and cancer cells, we compared Septin transcripts using PCR assays, Septin protein expression using Western blot, and Septin cellular expression using immunocytochemistry. We performed immunohistochemical analysis to examine whether Septin expression is increased in pancreatic cancer tissues compared to corresponding normal tissues. Silencing technology was used to test whether Septin expression is regulated by Chmp1A. Results: Our preliminary data indicates that the transcript and protein of Septins are increased in various pancreatic cancer cell lines compared to normal. Septin protein expression was increased or altered in human pancreatic ductal adenocarcinoma tissues compared to corresponding normal tissues. Additionally, our data implies that Chmp1A negatively regulates Septin expression, since Septin transcripts and proteins are increased when Chmp1A protein is silenced. Summary and future direction: Our data suggests that Septin functions as an oncogene in pancreatic cancer cells and that Chmp1A functions as a tumor suppressor partly by inhibiting the oncogenic action of Septin proteins. For the completion of the project in the future, we plan to confirm the function of Septins by investigating the effect of Septin overexpression on pancreatic cancer cell proliferation. In addition, we will further investigate the interaction between Septins and Chmp1A by examining Septin expression and localization in pancreatic cancer cells that overexpress Chmp1A. Citation Format: Mei Cai, Joseph Amor, Maiyon Park. Examining the potential oncogenic function of septins and their interaction with Chmp1A tumor suppressor in pancreatic cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5834.
Abstract 5776: Predictors of radioactive iodine refractoriness in papillary thyroid carcinomas
Authors: Tariq Masoodi, Sarah Siraj, Abdul K. Siraj, Saud Azam, Zeeshan Qadri, Sandeep K. Parvathareddy, Khawla S. Al-Kuraya
Journal: Cancer Research (2022)

Abstract Optimized surgery and radioactive iodine (131I, RAI) are the cornerstone of treatment for papillary thyroid carcinoma (PTC). Although standard treatment is curative for most, 5-20% of PTC patients develop RAI refractory disease – the main cause of thyroid cancer-related deaths. Early predictors indicating therapeutic response to RAI therapy in PTC are yet to be elucidated. We performed whole-exome sequencing (at a median depth of 198x) on 158 patient-matched primary PTCs and germline DNA. Clinical data was used to categorize RAI avidity in the PTC cohort. Whereby, 66 RAI refractory and 92 RAI avid tumors were identified. Clinical data and somatic variants were analyzed to compare the clinicopathological presentation, genomic landscape and mutational signatures between RAI refractory and avid PTCs. RAI refractory tumors were significantly associated with distinct aggressive clinicopathological features, including positive surgical margins (65.5% versus 26.7%; p=0.016) and the presence of lymph node metastases at primary diagnosis (62.5% versus 30.1%; p=0.012); higher nonsilent tumor mutation burden (p=0.011); and the enrichment of APOBEC-related single base substitution (SBS) COSMIC mutational signatures 2 (p=0.03) and 13 (p&amp;lt;0.001). APOBEC mutational signatures were not associated with BRAFV600E mutation. Notably, using multivariate logistic regression analysis only the SBS13 (odds ratio 13.01, 95% confidence intervals 1.20-140.94) APOBEC mutational signature was revealed to be an independent predictor of RAI refractoriness in PTC (p=0.035). Furthermore, using Cox proportional hazards SBS13-positive tumors (hazard ratio 3.52, 95% confidence intervals 1.79-6.91) were also significantly associated with poorer progression-free survival (p&amp;lt;0.001), albeit only in univariate analysis. This study highlights distinct clinical and genomic features in RAI refractory PTC, but above all proposes the APOBEC SBS13 mutational signature as an independent predictor of RAI refractoriness in a more aggressive subgroup of PTC. Where detection of RAI refractory disease following standard surgical PTC removal, and more suitable therapeutic interventions may potentially improve patient outcomes. Citation Format: Tariq Masoodi, Sarah Siraj, Abdul K. Siraj, Saud Azam, Zeeshan Qadri, Sandeep K. Parvathareddy, Khawla S. Al-Kuraya. Predictors of radioactive iodine refractoriness in papillary thyroid carcinomas [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5776.
Abstract 1509: Genome-wide CRISPR/Cas9 library screening identified THRAP3 as a critical driver for resistance to ATR inhibitor in sarcomas revealing synthetic lethality with ATM inhibition
Authors: Mariella Spalato, Audrey Laroche-Clary, Vanessa Chaire, Antoine Italiano
Journal: Cancer Research (2022)

Abstract Background: ATR plays a crucial role in maintaining genomic integrity by responding to a large spectrum of DNA damage, including double strand breaks (DSBs) that interfere with replication. We have previously demo started that ATR inhibition is associated with anti-tumor activity in pre-clinical models of soft-tissue sarcomas (STS) (Laroche et al., 2020). We decided to investigate the mechanisms of resistance to ATR inhibition in sarcomas. Methods: We used a CRISPRa was to identify genes that mediate resistance to AZD6738 in STS cells. The anti-tumor activity of AZD6738 (ATR inhibitor) and AZD0156 (ATM inhibitor) was investigated in a panel for 10 STS cell lines and two patient-derived xenografts (PDX) established at Institut Bergonié (Bordeaux, France). Results: We used a CRISPR approach in a STS cell line resistant to AZD6738 and we made a negative-selection screen, to identify genes whose silencing conferred sensitivity to low doses of ATR inhibition. Among these genes, we identified THRAP3 which encodes a protein phosphorylated in response to DNA damage and primarily by ATR. THRAP3 is involved in the maturation and further export of transcripts encoding the ATM and its depletion results in deficient processing of transcripts encoding the ATM kinase. We validate the result of our CRISPR analysis by demonstrating that selective THRAP3 inhibition reduce significantly ATRi IC50. Given the role of role of THRAP3 on the regulation of ATM activity, we decided to investigate the potential synergy between ATR and ATM inhibition in vivo and in vitro. AZD6738 and AZD0156 displayed a synergistic or additive effect in above all the STS cell lines tested. We noted that ATRi treatment reduced phosphorylation of the ATR kinase target CHK1 but increased ATM phosphorylation, suggesting that ATM pathway takes over for DNA Damage Response and cells survival. In contrast, both ATR and ATM pathway were inhibited when AZD6738 and AZD0156 were used in combination, as shown by reduction of CHK1 and ATM phosphorylation. We validated our in vitro results in an in vivo model of liposarcoma xenograft in which AZD6738 and AZD0156 had synergistic anti-tumor activity. Conclusion: Our study demonstrates synthetically lethal interactions between ATM and ATR in vitro and in vivo. This combination deserves further investigaitons in sarcomas. Citation Format: Mariella Spalato, Audrey Laroche-Clary, Vanessa Chaire, Antoine Italiano. Genome-wide CRISPR/Cas9 library screening identified THRAP3 as a critical driver for resistance to ATR inhibitor in sarcomas revealing synthetic lethality with ATM inhibition [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1509.
Abstract 1380: <i>Setdb1</i>-loss reactivates ERV expression and interferon signaling to induce immune-mediated melanoma clearance
Authors: Meaghan K. McGeary, William Damsky, Drew Daniels, Goran Micevic, Eric Song, Hua Jane Lou, Clotilde Calderwood, Sateja Paradkar, Akiko Iwasaki, David Calderwood, Benjamin Turk, Marcus Bosenberg
Journal: Cancer Research (2022)

Abstract While immunotherapies have been revolutionary for the treatment of many cancers including melanoma, most patients do not respond, or develop resistance to these therapies. Several epigenetic modulators have been identified as potential targets for augmenting anti-tumor immunity, however the full breadth of their role is not well-understood. To identify modulators of anti-tumor immunity in melanoma, we performed a whole-genome CRISPR screen using the YUMMER-G model and identified members of the HUSH complex and its associated methyltransferase, Setdb1, as drop-out hits. To validate these findings, we used CRISPR-Cas9 to knockout Setdb1 individually and observed that Setdb1-/- tumors are cleared by their host mice in a CD8+ T-cell dependent manner. To determine the source of immunogenicity in Setdb1-/- cells, we performed RNA-sequencing, cytokine profiling, and evaluated antigen presentation by flow cytometry. These assays revealed increased MHC-I levels, elevated secretion of Ifn-, and induction of an interferon-stimulated gene (ISG) expression program, consistent with the observed immunogenicity. We further determined that treating Setdb1-/- cells with IFNAR-blocking antibodies restores MHC-I levels to wild-type levels, suggestive of a tumor-intrinsic interferon loop. We hypothesized that type-I interferon signaling is generated through sensing of expressed endogenous retroviral elements (ERVs), and consistently observe upregulation of ERVs in Setdb1-/- cells. Previous studies have described the potential for ERV-derived antigens to act as substrates for anti-tumor activity by CD8+ T cells. We identified T cells in the tumor microenvironment of Setdb1-/- tumors that bind tetramer carrying the P15E peptide derived from ERV envelope. Together, these findings suggest that tumors lacking expression of Setdb1-/- upregulate ERV transcripts, driving expression of type-I interferons which generate an inflamed tumor microenvironment and potentiate efficient tumor clearance of Setdb1-/- tumors. Overall, this study emphasizes a critical role for regulators of ERV expression and type-I interferon expression, and suggests their potential as therapeutic targets for augmenting anti-cancer immune responses. Citation Format: Meaghan K. McGeary, William Damsky, Drew Daniels, Goran Micevic, Eric Song, Hua Jane Lou, Clotilde Calderwood, Sateja Paradkar, Akiko Iwasaki, David Calderwood, Benjamin Turk, Marcus Bosenberg. Setdb1-loss reactivates ERV expression and interferon signaling to induce immune-mediated melanoma clearance [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1380.
Abstract 6392: Predicting malignancy in indeterminate pulmonary nodules using quantitative CT imaging
Authors: Kate M. Bloch, Xingyi Shi, Fenghai Duan, George R. Washko, Avrum Spira, Denise R. Aberle, Raul S. Estepar, Ehab Billatos, Marc E. Lenburg
Journal: Cancer Research (2022)

Abstract With an increasing number of positive lung cancer screening trials and the growing utilization of low dose CT screening, the detection of indeterminate pulmonary nodules is an important clinical problem. A biomarker that will be able to differentiate between benign andmalignant nodules would help to accelerate diagnosis and reduce unnecessary and invasive procedures. Here, we investigated the utility of quantitative radiomics to predict malignancy of small pulmonary nodules. Data including cancer status, age, gender, smokingstatus and CT radiomics data, from 242 patients accrued from the Detection of Early Lung Cancer Among Military Personnel (DECAMP1) consortium was used. DECAMP1 is a prospective study of 500 current or former smokers with indeterminate pulmonary nodules (0.7-3.0 cm). A total of 446 quantitative radiomic features were extracted from CT images of each patient. For the prediction models, various feature selection methods and machine learning algorithms including Random Forest, Gradient Boosting Machine and Support Vector Machine were used. Data was split into train and test set with tenfold cross-validation.Models were evaluated using; Accuracy, Sensitivity, Specificity and Area under the curve - a receiver operating characteristic curve (AUC-ROC). In terms of predictive performance, the AUC value was 0.64 (95% CI: 0.50-0.78) for the clinical model and 0.77 (95% CI: 0.64-0.90) for the radiomics model. Adding clinical features to the radiomics model (gender, age, smoking status) did not improve the model. We have also investigated the slice thickness and scanner (PET vs PET-CT) variables on the models’ performance and saw a modest improvement of the AUC values when using more homogenous data. In this study, we showed the potential of radiomics for lung cancer prediction in DECAMP1.For future work, we are planning to test whether incorporating bronchial gene expression data improves lung cancer detection and to validate these findings in separate, independent cohorts. Citation Format: Kate M. Bloch, Xingyi Shi, Fenghai Duan, George R. Washko, Avrum Spira, Denise R. Aberle, Raul S. Estepar, Ehab Billatos, Marc E. Lenburg, on behalf of the DECAMP Investigators. Predicting malignancy in indeterminate pulmonary nodules using quantitative CT imaging [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 6392.
Abstract 888: Elucidating the mechanisms of eATP-induced changes in cell growth, energy metabolism, and cancer stem cells in human non-small lung cancer A549 cells
Authors: Jingwen Song, Xiaozhuo Chen
Journal: Cancer Research (2022)

Abstract The tumor microenvironment (TME) has concentrations of extracellular ATP (eATP) 103-104 times higher than normal healthy tissues, implying that eATP may have important roles in tumor development and progression. Our previous study, cited by a Nature Reviews Cancer paper, showed that the extracellular ATP (eATP) is internalized by tumors via macropinocytosis, a type of endocytosis, to increase intracellular ATP (iATP) levels and support tumor cells growth, drug resistance, and cancer cell movement by initiating epithelial to mesenchymal transition (EMT). Recently, our lab found that eATP functions in promoting cancer cell growth, metastasis are similar to those of TGF-β, a well-known EMT and cancer stem cells (CSCs) inducer. Increasing reports state that the EMT and CSCs share some molecular links, but the detailed mechanisms and inductor of them are still far from clear. In this report, eATP’s function in CSCs induction was investigated first. Result shows that eATP treatment significantly induces the protein expression level of CSC related makers, increases cell colony numbers, and cell populations with CSC markers expressed in human lung cancer A549 cells. In addition, RNA-sequencing analysis reveals the gene Stanniocalcin 1 (STC1) is significantly upregulated in both eATP and TGF-β treatments. STC1 gene has been reported to be a competitive biomarker in the tracking of cancers’ progressing. Besides, STC1 exhibits concentration-dependent stimulation effects on electron transportation chain (ETC) and respiration. However, the detail function of STC1 gene in eATP induced cell growth is unknown. To find out the mechanism, CRISPR-Cas9 technique was used to generate STC1 gene targeted knockout (STC1 KO) A549 cells. STC1 KO cells show slower cell growth rate, lower intracellular ATP level and lower oxygen consumption rate (OCR) when compared with normal A549 cells in vitro. These results strongly indicate STC1 gene involved in eATP induced cell growth by alteration iATP level and metabolic profile. Overall, this study not only unravels new role of eATP in CSC induction, but also provides new mechanism of eATP induced cell growth by altering the protein expression level of STC1. Citation Format: Jingwen Song, Xiaozhuo Chen. Elucidating the mechanisms of eATP-induced changes in cell growth, energy metabolism, and cancer stem cells in human non-small lung cancer A549 cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 888.
Abstract 74: Single-cell 3D spatial omics for tumor hypoxia
Authors: Yi-Chien Wu, Steve Seung-Young Lee
Journal: Cancer Research (2022)

Abstract Tumor hypoxia arises from the abnormal vasculature in tumors which limit the oxygen supply to the rapidly growing cancer cells. To acclimate to this deprived microenvironment, cancer cells upregulate hypoxia-inducible factor 1-alpha (HIF-1) signaling pathway priming themselves towards more aggressive and heterogeneous phenotypes. Hence, tumor hypoxia becomes a major obstacle for effective cancer treatment. Deciphering hypoxia-driven tumor heterogeneity within the tumors is essential to understanding cancer biology and developing novel therapeutic strategies. A stronger focus should be directed towards the effect of hypoxia types and levels rather than just the absence or presence of hypoxia since hypoxia is heterogeneous in the three-dimensional (3D) tumor microenvironment (TME). There are acute and chronic types of tumor hypoxia, and the hypoxia levels are also variable, forming unpredictable and irregular 3D hypoxic areas. Although traditional techniques (i.e., single-cell RNA sequencing (scRNA-seq), immunohistochemistry (IHC), and immunofluorescence (IF)) and innovative spatial transcriptomics have been developed and applied for investigating tumor cell heterogeneity. Underlying issue of missing spatial information, limited numbers of the biomarker detection, underrepresentation of 3D tumor structure, or limited analyzed area onto the array chip size exist respectively in these methods. The objective of this project is to develop a 3D spatial genomics approach with single-cell resolution, named sc3DSG, as an advanced spatial transcriptomic method to study hypoxia-driven cancer cell heterogeneity in 3D. Given that, I developed a 3D cellular fluorescence barcoding method by microscopic photobleaching in tumor macro-sections. The barcodes would maintain a fluorescent footprint of cells in different hypoxic areas upon tissue dissociation. Cells encoded with varied barcodes could be differentiated on flow cytometry and further sorted into separate groups for scRNA-seq. With the optimization with RNA preservation reagent in the workflow, sc3DSG achieves high-quality and high-yield RNA transcript for unbiased transcriptomic analysis. In summary, sc3DSG is an advanced spatial transcriptomic method including a sequential workflow of photobleaching barcoding, tissue dissociation, fluorescence-activated cell sorting (FACS), and scRNA-seq. Sc3DSG enables the study of tissue molecular features without losing spatial information and is a better fit for the study of complex 3D structure like vessels or tumor hypoxia. This approach will unravel hypoxia-driven bimolecular and cellular features by considering the degrees and types of tumor hypoxia. Citation Format: Yi-Chien Wu, Steve Seung-Young Lee. Single-cell 3D spatial omics for tumor hypoxia [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 74.
On the banks of the Vovcha and Kamyanka rivers: pages of the history of zemstvo medicine
Authors: M.P. Chaban, Z.I. Shevtsova, V.V. Gaponov, V.V. Gaponov
Journal: GASTROENTEROLOGY (2022)

The article considers the formation of Zemstvo medicine on the example of three villages of Alexander district in the Yekaterinoslav region. According to the latest reform, now it is the Synelnykiv district of the Dnipropetrovsk region. Historical and local lore information and stages of development of medical care in the villages of Havrylivka, Velykomykhailivka and Malomykhailivka have been presented. The article is illustrated with the materials about the life and professional path of Zemstvo doctors Pavlo Smirnov, Andrii Svechnikov, Yevhenia Vashchynenko, Mykola Khatetovsky, Maria Gamzagurdi and others.
Abstract 1849: Lipid metabolites as potential diagnostic biomarkers for stearoyl-CoA desaturase 1 targeting therapy in hepatocellular carcinoma (HCC)
Authors: Justyna Joanna Gleba
Journal: Cancer Research (2022)

Abstract New effective therapies should be developed for the treatment of hepatocellular carcinoma (HCC). One of the very promising strategies is blocking the activity of stearoyl-CoA desaturase 1 (SCD1). SCD1 is the enzyme responsible for de novo fatty acid (FAs) synthesis by converting saturated fatty acids (SFAs) into monounsaturated fatty acids (MUFAs). In our laboratory, we developed a novel, highly specific SCD1inhibitor - SSI-4. We have tested the biological activity of SSI-4 against different HCC cell lines and patient-derived xenografts (PDX) mouse models. Of the twelve tested HCC cell lines, four were highly sensitive to SSI-4 (IC50 1-50 nM). Other cell lines showed moderate or no sensitivity to SSI-4. We conducted analysis of the enzymatic protein levels involved in de novo fatty acid synthesis. Protein expression levels for these enzymes don’t predict response to therapy. To determine whether lipid metabolites predict response to SSI-4 therapy, lipidomic analysis was investigated. Our studies showed thatSSI-4 sensitive cells when exposed to SSI-4 had a higher baseline level of key lipid metabolites such as phospholipids (PL), diglycerides (DAG), diglycerides (TAG), ceramides (CE), and free fatty acids (FFA),compared to insensitive cells. We are currently validating these results in our in vivo models at the tumor tissue and blood levels. Additionally, mechanistic studies are in progress to determine if SREBP1c, an AKT regulated transcription factor known to regulate each of the fatty acid synthetic enzymes plays a role in HCC fatty acid synthesis and sensitivity to SCD1 inhibition. Citation Format: Justyna Joanna Gleba. Lipid metabolites as potential diagnostic biomarkers for stearoyl-CoA desaturase 1 targeting therapy in hepatocellular carcinoma (HCC) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1849.